HTSMultiQC-cleaning-report

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        Note that additional data was saved in HTSMultiQC-cleaning-report_multiqc_report_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.10.dev0

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        HTSMultiQC-cleaning-report

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2022-01-03, 17:42 based on data in: /share/dandekarlab/Houston/SCRI_Root_RNAseq_work/01-HTS_Preproc


        HTStream

        HTStream quality control and processing pipeline for High Throughput Sequencing data.

        hts_Stats

        Generates a JSON formatted file containing a set of statistical measures about the input read data.

        Showing 42/42 rows and 6/6 columns.
        Sample Name% PE% R1 Q30% R2 Q30GC ContentN ContentNotes
        29JM-11-1
        100.00%
        89.95%
        86.19%
        48.78%
        0.0000%
        initial stats
        29JM-11-2
        100.00%
        86.87%
        84.50%
        50.27%
        0.0000%
        initial stats
        29JM-11-3
        100.00%
        89.06%
        86.00%
        48.08%
        0.0000%
        initial stats
        29JM-11-4
        100.00%
        89.58%
        86.71%
        47.69%
        0.0000%
        initial stats
        29JM-11-5
        100.00%
        89.44%
        86.47%
        48.44%
        0.0000%
        initial stats
        29JM-11-6
        100.00%
        90.53%
        86.97%
        46.47%
        0.0000%
        initial stats
        JMS-12-1
        100.00%
        90.14%
        86.46%
        46.18%
        0.0000%
        initial stats
        JMS-12-2
        100.00%
        90.18%
        86.28%
        46.62%
        0.0000%
        initial stats
        JMS-12-3
        100.00%
        90.60%
        86.83%
        46.27%
        0.0000%
        initial stats
        JMS-12-4
        100.00%
        89.14%
        86.58%
        48.52%
        0.0000%
        initial stats
        JMS-12-5
        100.00%
        90.15%
        86.38%
        46.36%
        0.0000%
        initial stats
        JMS-12-6
        100.00%
        90.36%
        86.67%
        46.17%
        0.0000%
        initial stats
        MS1-122-1
        100.00%
        89.93%
        84.79%
        45.76%
        0.0000%
        initial stats
        MS1-122-2
        100.00%
        89.44%
        86.22%
        46.30%
        0.0000%
        initial stats
        MS1-122-3
        100.00%
        89.34%
        83.76%
        46.41%
        0.0000%
        initial stats
        MS1-122-4
        100.00%
        89.14%
        84.43%
        47.69%
        0.0000%
        initial stats
        MS1-122-5
        100.00%
        89.41%
        85.95%
        46.18%
        0.0000%
        initial stats
        MS1-122-6
        100.00%
        89.58%
        86.75%
        47.98%
        0.0000%
        initial stats
        MS1-36-1
        100.00%
        89.76%
        85.56%
        46.47%
        0.0000%
        initial stats
        MS1-36-2
        100.00%
        89.54%
        82.48%
        46.62%
        0.0000%
        initial stats
        MS1-36-3
        100.00%
        90.71%
        85.49%
        45.79%
        0.0000%
        initial stats
        MS1-36-4
        100.00%
        90.80%
        87.34%
        46.18%
        0.0000%
        initial stats
        MS1-36-5
        100.00%
        88.71%
        83.98%
        47.56%
        0.0000%
        initial stats
        MS1-36-6
        100.00%
        90.71%
        86.18%
        47.12%
        0.0000%
        initial stats
        MS1-41-1
        100.00%
        89.81%
        86.50%
        46.46%
        0.0000%
        initial stats
        MS1-41-2
        100.00%
        88.67%
        85.74%
        49.03%
        0.0000%
        initial stats
        MS1-41-3
        100.00%
        90.09%
        85.91%
        46.46%
        0.0000%
        initial stats
        MS1-41-4
        100.00%
        89.72%
        85.65%
        46.91%
        0.0000%
        initial stats
        MS1-41-5
        100.00%
        89.73%
        86.31%
        49.19%
        0.0000%
        initial stats
        MS1-41-6
        100.00%
        89.41%
        85.96%
        47.14%
        0.0000%
        initial stats
        MS1-56-1
        100.00%
        89.40%
        86.18%
        46.52%
        0.0000%
        initial stats
        MS1-56-2
        100.00%
        89.40%
        85.97%
        47.35%
        0.0000%
        initial stats
        MS1-56-3
        100.00%
        89.78%
        86.63%
        47.04%
        0.0000%
        initial stats
        MS1-56-4
        100.00%
        90.23%
        87.04%
        47.05%
        0.0000%
        initial stats
        MS1-56-5
        100.00%
        89.01%
        86.58%
        51.90%
        0.0000%
        initial stats
        MS1-56-6
        100.00%
        90.49%
        87.13%
        47.99%
        0.0000%
        initial stats
        STJM-4-1
        100.00%
        86.14%
        85.65%
        52.02%
        0.0000%
        initial stats
        STJM-4-2
        100.00%
        88.29%
        86.19%
        47.83%
        0.0000%
        initial stats
        STJM-4-3
        100.00%
        88.24%
        85.31%
        46.71%
        0.0000%
        initial stats
        STJM-4-4
        100.00%
        89.92%
        86.18%
        47.84%
        0.0000%
        initial stats
        STJM-4-5
        100.00%
        87.84%
        85.25%
        48.26%
        0.0000%
        initial stats
        STJM-4-6
        100.00%
        89.11%
        85.65%
        48.27%
        0.0000%
        initial stats

        Read Lengths: Paired End

        Distribution of read lengths for each sample.

        Notice: Each sample has a uniform read length distribution.
        Showing 42/42 rows and 2/2 columns.
        Sample NameR1 Read LengthsR2 Read Lengths
        29JM-11-1
        151
        151
        29JM-11-2
        151
        151
        29JM-11-3
        151
        151
        29JM-11-4
        151
        151
        29JM-11-5
        151
        151
        29JM-11-6
        151
        151
        JMS-12-1
        151
        151
        JMS-12-2
        151
        151
        JMS-12-3
        151
        151
        JMS-12-4
        151
        151
        JMS-12-5
        151
        151
        JMS-12-6
        151
        151
        MS1-122-1
        151
        151
        MS1-122-2
        151
        151
        MS1-122-3
        151
        151
        MS1-122-4
        151
        151
        MS1-122-5
        151
        151
        MS1-122-6
        151
        151
        MS1-36-1
        151
        151
        MS1-36-2
        151
        151
        MS1-36-3
        151
        151
        MS1-36-4
        151
        151
        MS1-36-5
        151
        151
        MS1-36-6
        151
        151
        MS1-41-1
        151
        151
        MS1-41-2
        151
        151
        MS1-41-3
        151
        151
        MS1-41-4
        151
        151
        MS1-41-5
        151
        151
        MS1-41-6
        151
        151
        MS1-56-1
        151
        151
        MS1-56-2
        151
        151
        MS1-56-3
        151
        151
        MS1-56-4
        151
        151
        MS1-56-5
        151
        151
        MS1-56-6
        151
        151
        STJM-4-1
        151
        151
        STJM-4-2
        151
        151
        STJM-4-3
        151
        151
        STJM-4-4
        151
        151
        STJM-4-5
        151
        151
        STJM-4-6
        151
        151

        Base by Cycle: Paired End

        Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.

        loading..

        Quality by Cycle: Paired End

        Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

        loading..

        hts_SeqScreener

        A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.

        Showing 42/42 rows and 3/3 columns.
        Sample NamePE hits% PE HitsNotes
        29JM-11-1
        1
        0.0000%
        screen phix
        29JM-11-2
        0
        0.0000%
        screen phix
        29JM-11-3
        0
        0.0000%
        screen phix
        29JM-11-4
        0
        0.0000%
        screen phix
        29JM-11-5
        0
        0.0000%
        screen phix
        29JM-11-6
        0
        0.0000%
        screen phix
        JMS-12-1
        0
        0.0000%
        screen phix
        JMS-12-2
        2
        0.0000%
        screen phix
        JMS-12-3
        0
        0.0000%
        screen phix
        JMS-12-4
        1
        0.0000%
        screen phix
        JMS-12-5
        3
        0.0000%
        screen phix
        JMS-12-6
        1
        0.0000%
        screen phix
        MS1-122-1
        0
        0.0000%
        screen phix
        MS1-122-2
        0
        0.0000%
        screen phix
        MS1-122-3
        0
        0.0000%
        screen phix
        MS1-122-4
        0
        0.0000%
        screen phix
        MS1-122-5
        0
        0.0000%
        screen phix
        MS1-122-6
        2
        0.0000%
        screen phix
        MS1-36-1
        0
        0.0000%
        screen phix
        MS1-36-2
        0
        0.0000%
        screen phix
        MS1-36-3
        0
        0.0000%
        screen phix
        MS1-36-4
        1
        0.0000%
        screen phix
        MS1-36-5
        0
        0.0000%
        screen phix
        MS1-36-6
        0
        0.0000%
        screen phix
        MS1-41-1
        0
        0.0000%
        screen phix
        MS1-41-2
        0
        0.0000%
        screen phix
        MS1-41-3
        0
        0.0000%
        screen phix
        MS1-41-4
        0
        0.0000%
        screen phix
        MS1-41-5
        0
        0.0000%
        screen phix
        MS1-41-6
        1
        0.0000%
        screen phix
        MS1-56-1
        0
        0.0000%
        screen phix
        MS1-56-2
        0
        0.0000%
        screen phix
        MS1-56-3
        0
        0.0000%
        screen phix
        MS1-56-4
        2
        0.0000%
        screen phix
        MS1-56-5
        1
        0.0000%
        screen phix
        MS1-56-6
        1
        0.0000%
        screen phix
        STJM-4-1
        0
        0.0000%
        screen phix
        STJM-4-2
        1
        0.0000%
        screen phix
        STJM-4-3
        0
        0.0000%
        screen phix
        STJM-4-4
        3
        0.0000%
        screen phix
        STJM-4-5
        0
        0.0000%
        screen phix
        STJM-4-6
        0
        0.0000%
        screen phix

        hts_SeqScreener 2

        A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.

        Showing 42/42 rows and 3/3 columns.
        Sample NamePE hits% PE HitsNotes
        29JM-11-1
        3093995
        21.6919%
        count the number of rRNA reads
        29JM-11-2
        4061581
        41.7823%
        count the number of rRNA reads
        29JM-11-3
        2926056
        24.6395%
        count the number of rRNA reads
        29JM-11-4
        3746781
        20.0501%
        count the number of rRNA reads
        29JM-11-5
        4634312
        27.0060%
        count the number of rRNA reads
        29JM-11-6
        239295
        1.1400%
        count the number of rRNA reads
        JMS-12-1
        172648
        1.2984%
        count the number of rRNA reads
        JMS-12-2
        547911
        4.9555%
        count the number of rRNA reads
        JMS-12-3
        808672
        5.1465%
        count the number of rRNA reads
        JMS-12-4
        3004810
        27.8810%
        count the number of rRNA reads
        JMS-12-5
        692571
        4.4940%
        count the number of rRNA reads
        JMS-12-6
        230864
        1.6761%
        count the number of rRNA reads
        MS1-122-1
        138010
        1.2019%
        count the number of rRNA reads
        MS1-122-2
        548745
        3.4746%
        count the number of rRNA reads
        MS1-122-3
        505136
        3.1594%
        count the number of rRNA reads
        MS1-122-4
        2801765
        15.7665%
        count the number of rRNA reads
        MS1-122-5
        719335
        3.8210%
        count the number of rRNA reads
        MS1-122-6
        4411886
        22.8508%
        count the number of rRNA reads
        MS1-36-1
        642047
        3.0498%
        count the number of rRNA reads
        MS1-36-2
        1477544
        6.3310%
        count the number of rRNA reads
        MS1-36-3
        328659
        1.5200%
        count the number of rRNA reads
        MS1-36-4
        339714
        2.6586%
        count the number of rRNA reads
        MS1-36-5
        1614528
        11.6100%
        count the number of rRNA reads
        MS1-36-6
        2975559
        11.1945%
        count the number of rRNA reads
        MS1-41-1
        2602501
        13.4520%
        count the number of rRNA reads
        MS1-41-2
        3546070
        27.8019%
        count the number of rRNA reads
        MS1-41-3
        314666
        2.9254%
        count the number of rRNA reads
        MS1-41-4
        395811
        4.0205%
        count the number of rRNA reads
        MS1-41-5
        5689857
        24.8027%
        count the number of rRNA reads
        MS1-41-6
        1580991
        10.0976%
        count the number of rRNA reads
        MS1-56-1
        474936
        2.6893%
        count the number of rRNA reads
        MS1-56-2
        1401384
        8.1975%
        count the number of rRNA reads
        MS1-56-3
        953551
        5.8386%
        count the number of rRNA reads
        MS1-56-4
        866827
        7.1640%
        count the number of rRNA reads
        MS1-56-5
        8185566
        62.0490%
        count the number of rRNA reads
        MS1-56-6
        3294702
        13.4853%
        count the number of rRNA reads
        STJM-4-1
        6421285
        61.4649%
        count the number of rRNA reads
        STJM-4-2
        672639
        4.2700%
        count the number of rRNA reads
        STJM-4-3
        190321
        1.9589%
        count the number of rRNA reads
        STJM-4-4
        1009984
        7.9049%
        count the number of rRNA reads
        STJM-4-5
        1374979
        10.2073%
        count the number of rRNA reads
        STJM-4-6
        1763251
        16.5958%
        count the number of rRNA reads

        hts_SuperDeduper

        A reference free duplicate read removal tool.

        Showing 42/42 rows and 3/3 columns.
        Sample Name% Duplicates% IgnoredNotes
        29JM-11-1
        76.94%
        0.00%
        remove PCR duplicates
        29JM-11-2
        88.32%
        0.00%
        remove PCR duplicates
        29JM-11-3
        68.00%
        0.00%
        remove PCR duplicates
        29JM-11-4
        65.30%
        0.00%
        remove PCR duplicates
        29JM-11-5
        55.68%
        0.00%
        remove PCR duplicates
        29JM-11-6
        58.92%
        0.00%
        remove PCR duplicates
        JMS-12-1
        57.40%
        0.00%
        remove PCR duplicates
        JMS-12-2
        52.06%
        0.00%
        remove PCR duplicates
        JMS-12-3
        57.80%
        0.00%
        remove PCR duplicates
        JMS-12-4
        52.85%
        0.00%
        remove PCR duplicates
        JMS-12-5
        56.14%
        0.00%
        remove PCR duplicates
        JMS-12-6
        39.00%
        0.00%
        remove PCR duplicates
        MS1-122-1
        50.35%
        0.00%
        remove PCR duplicates
        MS1-122-2
        50.99%
        0.00%
        remove PCR duplicates
        MS1-122-3
        48.44%
        0.00%
        remove PCR duplicates
        MS1-122-4
        72.74%
        0.00%
        remove PCR duplicates
        MS1-122-5
        40.25%
        0.00%
        remove PCR duplicates
        MS1-122-6
        73.14%
        0.00%
        remove PCR duplicates
        MS1-36-1
        57.28%
        0.00%
        remove PCR duplicates
        MS1-36-2
        72.32%
        0.00%
        remove PCR duplicates
        MS1-36-3
        34.10%
        0.00%
        remove PCR duplicates
        MS1-36-4
        46.29%
        0.00%
        remove PCR duplicates
        MS1-36-5
        64.75%
        0.00%
        remove PCR duplicates
        MS1-36-6
        65.12%
        0.00%
        remove PCR duplicates
        MS1-41-1
        62.24%
        0.00%
        remove PCR duplicates
        MS1-41-2
        66.74%
        0.00%
        remove PCR duplicates
        MS1-41-3
        45.55%
        0.00%
        remove PCR duplicates
        MS1-41-4
        45.78%
        0.00%
        remove PCR duplicates
        MS1-41-5
        67.23%
        0.00%
        remove PCR duplicates
        MS1-41-6
        62.07%
        0.00%
        remove PCR duplicates
        MS1-56-1
        59.95%
        0.00%
        remove PCR duplicates
        MS1-56-2
        61.34%
        0.00%
        remove PCR duplicates
        MS1-56-3
        57.05%
        0.00%
        remove PCR duplicates
        MS1-56-4
        54.76%
        0.00%
        remove PCR duplicates
        MS1-56-5
        79.39%
        0.00%
        remove PCR duplicates
        MS1-56-6
        62.21%
        0.00%
        remove PCR duplicates
        STJM-4-1
        89.31%
        0.00%
        remove PCR duplicates
        STJM-4-2
        81.81%
        0.00%
        remove PCR duplicates
        STJM-4-3
        83.16%
        0.00%
        remove PCR duplicates
        STJM-4-4
        69.37%
        0.00%
        remove PCR duplicates
        STJM-4-5
        85.72%
        0.00%
        remove PCR duplicates
        STJM-4-6
        78.60%
        0.00%
        remove PCR duplicates

        SuperDeduper: Duplicate Saturation

        Plots the number of duplicates against the number of unique reads per sample.

        loading..

        hts_AdapterTrimmer

        Trims adapters which are sequenced when the fragment insert length is shorter than the read length.

        Showing 42/42 rows and 4/4 columns.
        Sample Name% Bp Lost% AdaptersAvg. Bps TrimmedNotes
        29JM-11-1
        4.99%
        44.71%
        33.67
        trim adapters
        29JM-11-2
        1.92%
        17.47%
        33.10
        trim adapters
        29JM-11-3
        5.35%
        46.86%
        34.47
        trim adapters
        29JM-11-4
        4.87%
        43.24%
        34.02
        trim adapters
        29JM-11-5
        4.89%
        44.18%
        33.41
        trim adapters
        29JM-11-6
        4.57%
        42.20%
        32.69
        trim adapters
        JMS-12-1
        5.31%
        47.35%
        33.85
        trim adapters
        JMS-12-2
        3.83%
        37.89%
        30.50
        trim adapters
        JMS-12-3
        5.58%
        51.62%
        32.65
        trim adapters
        JMS-12-4
        6.82%
        60.13%
        34.28
        trim adapters
        JMS-12-5
        5.65%
        52.14%
        32.74
        trim adapters
        JMS-12-6
        3.85%
        34.85%
        33.35
        trim adapters
        MS1-122-1
        5.35%
        47.52%
        34.01
        trim adapters
        MS1-122-2
        3.95%
        35.16%
        33.94
        trim adapters
        MS1-122-3
        3.01%
        27.39%
        33.14
        trim adapters
        MS1-122-4
        3.73%
        33.25%
        33.85
        trim adapters
        MS1-122-5
        3.43%
        30.58%
        33.88
        trim adapters
        MS1-122-6
        4.29%
        39.96%
        32.39
        trim adapters
        MS1-36-1
        3.07%
        30.08%
        30.82
        trim adapters
        MS1-36-2
        4.01%
        37.71%
        32.15
        trim adapters
        MS1-36-3
        4.08%
        37.45%
        32.94
        trim adapters
        MS1-36-4
        6.61%
        59.95%
        33.32
        trim adapters
        MS1-36-5
        2.92%
        27.10%
        32.53
        trim adapters
        MS1-36-6
        3.61%
        31.80%
        34.29
        trim adapters
        MS1-41-1
        5.61%
        49.56%
        34.20
        trim adapters
        MS1-41-2
        4.68%
        41.18%
        34.29
        trim adapters
        MS1-41-3
        4.39%
        40.28%
        32.90
        trim adapters
        MS1-41-4
        4.24%
        37.93%
        33.72
        trim adapters
        MS1-41-5
        4.09%
        36.70%
        33.69
        trim adapters
        MS1-41-6
        4.01%
        35.78%
        33.82
        trim adapters
        MS1-56-1
        3.16%
        30.22%
        31.62
        trim adapters
        MS1-56-2
        3.65%
        34.03%
        32.41
        trim adapters
        MS1-56-3
        4.63%
        42.25%
        33.10
        trim adapters
        MS1-56-4
        5.11%
        48.52%
        31.79
        trim adapters
        MS1-56-5
        4.00%
        36.64%
        33.01
        trim adapters
        MS1-56-6
        4.09%
        38.09%
        32.40
        trim adapters
        STJM-4-1
        2.32%
        21.79%
        32.22
        trim adapters
        STJM-4-2
        3.28%
        29.96%
        33.09
        trim adapters
        STJM-4-3
        2.57%
        24.14%
        32.12
        trim adapters
        STJM-4-4
        3.58%
        32.58%
        33.16
        trim adapters
        STJM-4-5
        3.25%
        30.31%
        32.40
        trim adapters
        STJM-4-6
        4.05%
        37.18%
        32.86
        trim adapters

        AdapterTrimmer: Trimmed Basepairs Composition

        Composition of basepairs trimmed from the ends of paired end and single end reads.

        loading..

        hts_PolyATTrim

        Attempts to trim poly-A and poly-T sequences from the end of reads.

        Showing 42/42 rows and 4/4 columns.
        Sample NameTotal Bp Lost% R1 of Bp Lost% R2 of Bp LostNotes
        29JM-11-1
        25189
        0.00%
        100.00%
        remove polyAT tails
        29JM-11-2
        11035
        0.00%
        100.00%
        remove polyAT tails
        29JM-11-3
        40364
        0.00%
        100.00%
        remove polyAT tails
        29JM-11-4
        76357
        0.00%
        100.00%
        remove polyAT tails
        29JM-11-5
        85171
        0.00%
        100.00%
        remove polyAT tails
        29JM-11-6
        100950
        0.00%
        100.00%
        remove polyAT tails
        JMS-12-1
        67682
        0.00%
        100.00%
        remove polyAT tails
        JMS-12-2
        61972
        0.00%
        100.00%
        remove polyAT tails
        JMS-12-3
        84637
        0.00%
        100.00%
        remove polyAT tails
        JMS-12-4
        65092
        0.00%
        100.00%
        remove polyAT tails
        JMS-12-5
        88380
        0.00%
        100.00%
        remove polyAT tails
        JMS-12-6
        106881
        0.00%
        100.00%
        remove polyAT tails
        MS1-122-1
        56933
        0.00%
        100.00%
        remove polyAT tails
        MS1-122-2
        79320
        0.00%
        100.00%
        remove polyAT tails
        MS1-122-3
        90020
        0.00%
        100.00%
        remove polyAT tails
        MS1-122-4
        42163
        0.00%
        100.00%
        remove polyAT tails
        MS1-122-5
        120556
        0.00%
        100.00%
        remove polyAT tails
        MS1-122-6
        52842
        0.00%
        100.00%
        remove polyAT tails
        MS1-36-1
        112492
        0.00%
        100.00%
        remove polyAT tails
        MS1-36-2
        79717
        0.00%
        100.00%
        remove polyAT tails
        MS1-36-3
        191250
        0.00%
        100.00%
        remove polyAT tails
        MS1-36-4
        81856
        0.00%
        100.00%
        remove polyAT tails
        MS1-36-5
        46937
        0.00%
        100.00%
        remove polyAT tails
        MS1-36-6
        81022
        0.00%
        100.00%
        remove polyAT tails
        MS1-41-1
        64490
        0.00%
        100.00%
        remove polyAT tails
        MS1-41-2
        34000
        0.00%
        100.00%
        remove polyAT tails
        MS1-41-3
        57790
        0.00%
        100.00%
        remove polyAT tails
        MS1-41-4
        54140
        0.00%
        100.00%
        remove polyAT tails
        MS1-41-5
        63013
        0.00%
        100.00%
        remove polyAT tails
        MS1-41-6
        57626
        0.00%
        100.00%
        remove polyAT tails
        MS1-56-1
        90586
        0.00%
        100.00%
        remove polyAT tails
        MS1-56-2
        78266
        0.00%
        100.00%
        remove polyAT tails
        MS1-56-3
        85127
        0.00%
        100.00%
        remove polyAT tails
        MS1-56-4
        58196
        0.00%
        100.00%
        remove polyAT tails
        MS1-56-5
        20103
        0.00%
        100.00%
        remove polyAT tails
        MS1-56-6
        99142
        0.00%
        100.00%
        remove polyAT tails
        STJM-4-1
        7725
        0.00%
        100.00%
        remove polyAT tails
        STJM-4-2
        29193
        0.00%
        100.00%
        remove polyAT tails
        STJM-4-3
        20113
        0.00%
        100.00%
        remove polyAT tails
        STJM-4-4
        41296
        0.00%
        100.00%
        remove polyAT tails
        STJM-4-5
        18833
        0.00%
        100.00%
        remove polyAT tails
        STJM-4-6
        22744
        0.00%
        100.00%
        remove polyAT tails

        hts_NTrimmer

        Trims reads to the longest subsequence that contains no N's.

        Showing 42/42 rows and 5/5 columns.
        Sample NameTotal Bp Lost% R1 of Bp Lost% R2 of Bp Lost% DiscardedNotes
        29JM-11-1
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        29JM-11-2
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        29JM-11-3
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        29JM-11-4
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        29JM-11-5
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        29JM-11-6
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        JMS-12-1
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        JMS-12-2
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        JMS-12-3
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        JMS-12-4
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        JMS-12-5
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        JMS-12-6
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-122-1
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-122-2
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-122-3
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-122-4
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-122-5
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-122-6
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-36-1
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-36-2
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-36-3
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-36-4
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-36-5
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-36-6
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-41-1
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-41-2
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-41-3
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-41-4
        -1
        -0.00%
        100.00%
        0.00%
        remove any remaining N characters
        MS1-41-5
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-41-6
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-56-1
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-56-2
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-56-3
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-56-4
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-56-5
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        MS1-56-6
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        STJM-4-1
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        STJM-4-2
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        STJM-4-3
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        STJM-4-4
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        STJM-4-5
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters
        STJM-4-6
        0
        0.00%
        0.00%
        0.00%
        remove any remaining N characters

        NTrimmer: Trimmed Basepairs Composition

        Plots the number of N bases trimmed from ends of paired end and single end reads.

        loading..

        hts_QWindowTrim

        Uses a sliding window approach to remove the low quality ends of reads.

        Showing 42/42 rows and 5/5 columns.
        Sample Name% Bp Lost% R1 of Bp Lost% R2 of Bp LostAvg. Bps TrimmedNotes
        29JM-11-1
        0.48%
        18.72%
        81.28%
        1.38
        quality trim the ends of reads
        29JM-11-2
        0.69%
        18.70%
        81.30%
        2.03
        quality trim the ends of reads
        29JM-11-3
        0.33%
        23.14%
        76.86%
        0.94
        quality trim the ends of reads
        29JM-11-4
        0.22%
        31.36%
        68.64%
        0.63
        quality trim the ends of reads
        29JM-11-5
        0.24%
        28.38%
        71.62%
        0.69
        quality trim the ends of reads
        29JM-11-6
        0.23%
        30.91%
        69.09%
        0.65
        quality trim the ends of reads
        JMS-12-1
        0.25%
        26.21%
        73.79%
        0.72
        quality trim the ends of reads
        JMS-12-2
        0.27%
        26.39%
        73.61%
        0.78
        quality trim the ends of reads
        JMS-12-3
        0.24%
        28.49%
        71.51%
        0.70
        quality trim the ends of reads
        JMS-12-4
        0.24%
        27.58%
        72.42%
        0.69
        quality trim the ends of reads
        JMS-12-5
        0.25%
        27.58%
        72.42%
        0.72
        quality trim the ends of reads
        JMS-12-6
        0.20%
        34.01%
        65.99%
        0.57
        quality trim the ends of reads
        MS1-122-1
        0.33%
        21.48%
        78.52%
        0.94
        quality trim the ends of reads
        MS1-122-2
        0.20%
        32.66%
        67.34%
        0.58
        quality trim the ends of reads
        MS1-122-3
        0.20%
        31.14%
        68.86%
        0.60
        quality trim the ends of reads
        MS1-122-4
        0.28%
        27.82%
        72.18%
        0.83
        quality trim the ends of reads
        MS1-122-5
        0.19%
        34.34%
        65.66%
        0.54
        quality trim the ends of reads
        MS1-122-6
        0.28%
        30.06%
        69.94%
        0.81
        quality trim the ends of reads
        MS1-36-1
        0.24%
        30.07%
        69.93%
        0.70
        quality trim the ends of reads
        MS1-36-2
        0.32%
        28.01%
        71.99%
        0.93
        quality trim the ends of reads
        MS1-36-3
        0.22%
        31.88%
        68.12%
        0.63
        quality trim the ends of reads
        MS1-36-4
        0.24%
        25.23%
        74.77%
        0.69
        quality trim the ends of reads
        MS1-36-5
        0.25%
        31.41%
        68.59%
        0.73
        quality trim the ends of reads
        MS1-36-6
        0.29%
        26.46%
        73.54%
        0.85
        quality trim the ends of reads
        MS1-41-1
        0.25%
        31.08%
        68.92%
        0.72
        quality trim the ends of reads
        MS1-41-2
        0.32%
        24.78%
        75.22%
        0.93
        quality trim the ends of reads
        MS1-41-3
        0.27%
        25.50%
        74.50%
        0.79
        quality trim the ends of reads
        MS1-41-4
        0.25%
        26.88%
        73.12%
        0.72
        quality trim the ends of reads
        MS1-41-5
        0.27%
        28.21%
        71.79%
        0.79
        quality trim the ends of reads
        MS1-41-6
        0.27%
        27.84%
        72.16%
        0.79
        quality trim the ends of reads
        MS1-56-1
        0.27%
        30.69%
        69.31%
        0.78
        quality trim the ends of reads
        MS1-56-2
        0.25%
        32.78%
        67.22%
        0.71
        quality trim the ends of reads
        MS1-56-3
        0.23%
        30.84%
        69.16%
        0.67
        quality trim the ends of reads
        MS1-56-4
        0.24%
        27.01%
        72.99%
        0.68
        quality trim the ends of reads
        MS1-56-5
        0.38%
        27.69%
        72.31%
        1.11
        quality trim the ends of reads
        MS1-56-6
        0.25%
        31.93%
        68.07%
        0.74
        quality trim the ends of reads
        STJM-4-1
        0.65%
        22.38%
        77.62%
        1.91
        quality trim the ends of reads
        STJM-4-2
        0.32%
        29.61%
        70.39%
        0.93
        quality trim the ends of reads
        STJM-4-3
        0.53%
        18.56%
        81.44%
        1.55
        quality trim the ends of reads
        STJM-4-4
        0.26%
        27.98%
        72.02%
        0.77
        quality trim the ends of reads
        STJM-4-5
        0.52%
        21.66%
        78.34%
        1.53
        quality trim the ends of reads
        STJM-4-6
        0.48%
        19.27%
        80.73%
        1.38
        quality trim the ends of reads

        QWindowTrim: Trimmed Basepairs Composition

        Plots the number of low quality basepairs trimmed from ends of paired end and single end reads.

           
        loading..

        hts_LengthFilter

        Discards reads below a minimum length threshold.

        Showing 42/42 rows and 2/2 columns.
        Sample Name% PE LostNotes
        29JM-11-1
        0.13%
        remove reads < 50bp
        29JM-11-2
        0.26%
        remove reads < 50bp
        29JM-11-3
        0.09%
        remove reads < 50bp
        29JM-11-4
        0.04%
        remove reads < 50bp
        29JM-11-5
        0.06%
        remove reads < 50bp
        29JM-11-6
        0.04%
        remove reads < 50bp
        JMS-12-1
        0.06%
        remove reads < 50bp
        JMS-12-2
        0.07%
        remove reads < 50bp
        JMS-12-3
        0.05%
        remove reads < 50bp
        JMS-12-4
        0.05%
        remove reads < 50bp
        JMS-12-5
        0.06%
        remove reads < 50bp
        JMS-12-6
        0.03%
        remove reads < 50bp
        MS1-122-1
        0.12%
        remove reads < 50bp
        MS1-122-2
        0.04%
        remove reads < 50bp
        MS1-122-3
        0.04%
        remove reads < 50bp
        MS1-122-4
        0.05%
        remove reads < 50bp
        MS1-122-5
        0.03%
        remove reads < 50bp
        MS1-122-6
        0.05%
        remove reads < 50bp
        MS1-36-1
        0.05%
        remove reads < 50bp
        MS1-36-2
        0.06%
        remove reads < 50bp
        MS1-36-3
        0.04%
        remove reads < 50bp
        MS1-36-4
        0.07%
        remove reads < 50bp
        MS1-36-5
        0.05%
        remove reads < 50bp
        MS1-36-6
        0.06%
        remove reads < 50bp
        MS1-41-1
        0.05%
        remove reads < 50bp
        MS1-41-2
        0.08%
        remove reads < 50bp
        MS1-41-3
        0.07%
        remove reads < 50bp
        MS1-41-4
        0.07%
        remove reads < 50bp
        MS1-41-5
        0.05%
        remove reads < 50bp
        MS1-41-6
        0.06%
        remove reads < 50bp
        MS1-56-1
        0.05%
        remove reads < 50bp
        MS1-56-2
        0.04%
        remove reads < 50bp
        MS1-56-3
        0.05%
        remove reads < 50bp
        MS1-56-4
        0.06%
        remove reads < 50bp
        MS1-56-5
        0.06%
        remove reads < 50bp
        MS1-56-6
        0.04%
        remove reads < 50bp
        STJM-4-1
        0.15%
        remove reads < 50bp
        STJM-4-2
        0.06%
        remove reads < 50bp
        STJM-4-3
        0.18%
        remove reads < 50bp
        STJM-4-4
        0.05%
        remove reads < 50bp
        STJM-4-5
        0.17%
        remove reads < 50bp
        STJM-4-6
        0.14%
        remove reads < 50bp

        hts_Stats 2

        Generates a JSON formatted file containing a set of statistical measures about the input read data.

        Showing 42/42 rows and 6/6 columns.
        Sample Name% PE% R1 Q30% R2 Q30GC ContentN ContentNotes
        29JM-11-1
        100.00%
        93.68%
        88.40%
        47.82%
        0.0000%
        final stats
        29JM-11-2
        100.00%
        90.32%
        84.23%
        48.40%
        0.0000%
        final stats
        29JM-11-3
        100.00%
        94.22%
        90.62%
        46.45%
        0.0000%
        final stats
        29JM-11-4
        100.00%
        94.65%
        91.86%
        46.20%
        0.0000%
        final stats
        29JM-11-5
        100.00%
        94.73%
        91.86%
        46.31%
        0.0000%
        final stats
        29JM-11-6
        100.00%
        95.01%
        91.84%
        46.48%
        0.0000%
        final stats
        JMS-12-1
        100.00%
        94.99%
        91.86%
        45.83%
        0.0000%
        final stats
        JMS-12-2
        100.00%
        94.83%
        91.57%
        46.36%
        0.0000%
        final stats
        JMS-12-3
        100.00%
        95.16%
        91.95%
        46.01%
        0.0000%
        final stats
        JMS-12-4
        100.00%
        95.35%
        92.19%
        45.74%
        0.0000%
        final stats
        JMS-12-5
        100.00%
        95.06%
        92.00%
        45.77%
        0.0000%
        final stats
        JMS-12-6
        100.00%
        94.68%
        91.91%
        45.85%
        0.0000%
        final stats
        MS1-122-1
        100.00%
        94.77%
        90.76%
        45.34%
        0.0000%
        final stats
        MS1-122-2
        100.00%
        94.45%
        91.89%
        45.83%
        0.0000%
        final stats
        MS1-122-3
        100.00%
        94.22%
        90.27%
        45.95%
        0.0000%
        final stats
        MS1-122-4
        100.00%
        93.46%
        89.40%
        47.12%
        0.0000%
        final stats
        MS1-122-5
        100.00%
        94.19%
        91.57%
        45.65%
        0.0000%
        final stats
        MS1-122-6
        100.00%
        94.13%
        90.67%
        46.96%
        0.0000%
        final stats
        MS1-36-1
        100.00%
        94.38%
        90.77%
        46.02%
        0.0000%
        final stats
        MS1-36-2
        100.00%
        93.73%
        88.40%
        46.49%
        0.0000%
        final stats
        MS1-36-3
        100.00%
        94.72%
        90.91%
        45.28%
        0.0000%
        final stats
        MS1-36-4
        100.00%
        95.72%
        92.84%
        45.43%
        0.0000%
        final stats
        MS1-36-5
        100.00%
        93.82%
        89.88%
        46.52%
        0.0000%
        final stats
        MS1-36-6
        100.00%
        93.91%
        89.79%
        46.32%
        0.0000%
        final stats
        MS1-41-1
        100.00%
        94.78%
        91.22%
        46.08%
        0.0000%
        final stats
        MS1-41-2
        100.00%
        94.07%
        90.30%
        47.47%
        0.0000%
        final stats
        MS1-41-3
        100.00%
        94.68%
        91.18%
        46.14%
        0.0000%
        final stats
        MS1-41-4
        100.00%
        94.50%
        91.29%
        46.55%
        0.0000%
        final stats
        MS1-41-5
        100.00%
        94.10%
        90.61%
        47.18%
        0.0000%
        final stats
        MS1-41-6
        100.00%
        94.19%
        90.69%
        46.38%
        0.0000%
        final stats
        MS1-56-1
        100.00%
        94.05%
        90.70%
        46.04%
        0.0000%
        final stats
        MS1-56-2
        100.00%
        94.17%
        90.72%
        46.51%
        0.0000%
        final stats
        MS1-56-3
        100.00%
        94.70%
        91.80%
        46.41%
        0.0000%
        final stats
        MS1-56-4
        100.00%
        95.36%
        92.56%
        46.50%
        0.0000%
        final stats
        MS1-56-5
        100.00%
        92.66%
        88.84%
        49.44%
        0.0000%
        final stats
        MS1-56-6
        100.00%
        94.45%
        91.09%
        46.94%
        0.0000%
        final stats
        STJM-4-1
        100.00%
        90.04%
        84.28%
        50.21%
        0.0000%
        final stats
        STJM-4-2
        100.00%
        93.27%
        89.48%
        47.37%
        0.0000%
        final stats
        STJM-4-3
        100.00%
        92.42%
        87.08%
        46.87%
        0.0000%
        final stats
        STJM-4-4
        100.00%
        94.28%
        90.76%
        47.31%
        0.0000%
        final stats
        STJM-4-5
        100.00%
        91.91%
        86.87%
        47.89%
        0.0000%
        final stats
        STJM-4-6
        100.00%
        93.30%
        88.29%
        47.82%
        0.0000%
        final stats

        Read Lengths: Paired End

        Distribution of read lengths for each sample.

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        Base by Cycle: Paired End

        Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.

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        Quality by Cycle: Paired End

        Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

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